Variant chr5-55851624-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_139017.7(IL31RA):c.54G>A(p.Pro18=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00829 in 1,613,812 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0062 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0085 ( 69 hom. )

Consequence

IL31RA
NM_139017.7 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.04

Variant links:

Genes affected

IL31RA (HGNC:18969): (interleukin 31 receptor A) The protein encoded by this gene belongs to the type I cytokine receptor family. This receptor, with homology to gp130, is expressed on monocytes, and is involved in IL-31 signaling via activation of STAT-3 and STAT-5. It functions either as a monomer, or as part of a receptor complex with oncostatin M receptor (OSMR). Several alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]

IL31RA links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 5-55851624-G-A is Benign according to our data. Variant chr5-55851624-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 790791.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.04 with no splicing effect.

BS2

High AC in GnomAd4 at 941 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IL31RA	NM_139017.7 linkuse as main transcript	c.54G>A	p.Pro18=	synonymous_variant	1/15	ENST00000652347.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IL31RA	ENST00000652347.2 linkuse as main transcript	c.54G>A	p.Pro18=	synonymous_variant	1/15		NM_139017.7	A2	Q8NI17-2

Frequencies

GnomAD3 genomes

AF:

0.00619

AC:

941

AN:

152070

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00169

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00229

Gnomad ASJ

AF:

0.00547

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000831

Gnomad FIN

AF:

0.0139

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00960

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00685

AC:

1685

AN:

246130

Hom.:

AF XY:

0.00680

AC XY:

910

AN XY:

133804

show subpopulations

Gnomad AFR exome

AF:

0.00155

Gnomad AMR exome

AF:

0.00293

Gnomad ASJ exome

AF:

0.00618

Gnomad EAS exome

AF:

0.000167

Gnomad SAS exome

AF:

0.00124

Gnomad FIN exome

AF:

0.0149

Gnomad NFE exome

AF:

0.00991

Gnomad OTH exome

AF:

0.00748

GnomAD4 exome

AF:

0.00851

AC:

12432

AN:

1461624

Hom.:

Cov.:

AF XY:

0.00824

AC XY:

5988

AN XY:

727126

show subpopulations

Gnomad4 AFR exome

AF:

0.00176

Gnomad4 AMR exome

AF:

0.00320

Gnomad4 ASJ exome

AF:

0.00486

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.000881

Gnomad4 FIN exome

AF:

0.0145

Gnomad4 NFE exome

AF:

0.00978

Gnomad4 OTH exome

AF:

0.00596

GnomAD4 genome

AF:

0.00618

AC:

941

AN:

152188

Hom.:

Cov.:

AF XY:

0.00622

AC XY:

463

AN XY:

74412

show subpopulations

Gnomad4 AFR

AF:

0.00169

Gnomad4 AMR

AF:

0.00229

Gnomad4 ASJ

AF:

0.00547

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000832

Gnomad4 FIN

AF:

0.0139

Gnomad4 NFE

AF:

0.00960

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00872

Hom.:

Bravo

AF:

0.00534

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00813

EpiControl

AF:

0.00913

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2024	IL31RA: BP4, BP7, BS2 -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.9

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over